Degree Of Inbreeding Research Articles

Effects of floral neighborhood on seed set and degree of outbreeding in a high-alpine cushion plant

Plants flowering together may influence each other's pollination and fecundity over a range of physical distances. Their effects on one another can be competitive, neutral, or facilitative. We manipulated the floral neighborhood of the high-alpine cushion plant Eritrichium nanum in the Swiss Alps and measured the effects of co-flowering neighbors on both the number of seeds produced and the degree of inbreeding and outbreeding in the offspring, as deduced from nuclear microsatellite markers. Seed set of E. nanum did not vary significantly with the presence or absence of two Saxifraga species growing as near neighbors, but it was higher in E. nanum cushions growing at low conspecific density than in those growing at high density. In addition, floral neighborhood had no detectable effect on the degree of selfing of E. nanum, but seeds from cushions growing at low conspecific density were more highly outbred than seeds from cushions at high density. Thus, there was no evidence of either competition or facilitation between E. nanum and Saxifraga spp. as mediated by pollinators at the spatial scale of our experimental manipulation. In contrast, the greater fecundity of E. nanum cushions at low density was consistent with reduced intraspecific competition for pollinators and might also represent a beneficial effect of highly outbred seeds as brought about by more long-distance pollinator flights under low-density conditions.

Ophthalmic findings in the Greek isolate of Cohen syndrome

A high frequency of the Cohen syndrome has been observed in a Greek island with 2,000 inhabitants and a high degree of inbreeding. All patients were homozygous for a COH1, exon 6-16 deletion suggesting a founder effect. We present the results of their first systematic ophthalmologic assessment. Myopia and chorioretinal atrophy were present in all patients of this cohort. Yet, in contrast to all groups previously reported, the majority presented with corneal changes, independently from age, gender, and family history. A pair of sisters, aged 11 and 15 years old, presented with bilateral keratoconus. More frequently (86%) than in any other ethnic group, Greek patients had cataracts that were bilateral and often graded as high as 3, even at a young age. As a whole, the ophthalmic phenotype of the Greek isolate of Cohen syndrome is characterized by the involvement of both the posterior and the anterior eye segment, bilaterally, in the majority of cases (93%). Greek Cohen patients that share a founder mutation are at a higher risk of developing blindness in respect to those of other ethnicities and genotypes. This study highlighted the need for pachymetry measurement as a means of surveillance and prediction of the visual impairment frequently observed.

Mitogenomic and microsatellite variation in descendants of the founder population of Newfoundland: high genetic diversity in an historically isolated population

The island of Newfoundland, the first of England's overseas colonies, was settled from the 17th century onward by restricted numbers of English, Irish, and French immigrants, in small "outport" communities that have maintained geographic, religious, and linguistic isolation to the latest generations. To measure the extent of modification and loss of genetic variation through founder effect, drift, and inbreeding in this historically isolated population, we analyzed the complete mitochondrial DNA (mtDNA) genomes and 14 microsatellite loci from each of 27 individuals with matrilineal ancestries extending to the colonial period. Every individual has a unique mtDNA genome sequence. All but one of these genomes are assignable to one of five major (H,J,K,T, and U) or minor (I) European haplogroups. The possibility of homoplasy at single nucleotide polymorphism (SNP) sites that define subtypes within the H haplogroup is discussed. Observed haplogroup proportions do not differ significantly from those of western Europeans or between English and Irish Newfoundlanders. The exceptional individual is a member of haplogroup A2, who appears to be the descendant of a Mi'kmaq First Nations mother and a French father, a common marriage pattern in the early settlement of Newfoundland. Microsatellite diversity is high (HE = 0.763), unstructured with respect to mtDNA haplotype or ethnicity, and there is no evidence of linkage disequilibrium. There is a small but significant degree of inbreeding (FIS = 0.0174). Collection of whole mtDNA genome data was facilitated by the use of microarray sequencing, and we describe a simple algorithm that is 99.67% efficient for sequence recovery.

The effects of age and environment on the expression of inbreeding depression in Eucalyptus globulus

Inbreeding adversely affects fitness traits in many plant and animal species, and the magnitude, stability and genetic basis of inbreeding depression (ID) will have short- and long-term evolutionary consequences. The effects of four degrees of inbreeding (selfing, f=50%; full- and half-sib matings, f=25 and 12.5%; and unrelated outcrosses, f=0%) on survival and growth of an island population of Eucalyptus globulus were studied at two sites for over 14 years. For selfs, ID in survival increased over time, reaching a maximum of 49% by age 14 years. However, their inbreeding depression for stem diameter remained relatively stable with age, and ranged from 28 to 36% across years and sites. ID for survival was markedly greater on the more productive site, possibly due to greater and earlier onset of inter-tree competition, but was similar on both sites for the diameter of survivors. The deleterious trait response to increasing inbreeding coefficients was linear for survival and diameter. Non-significant quadratic effects suggested that epistasis did not contribute considerably to the observed ID at the population level. Among- and within-family coefficients of variation for diameter increased with inbreeding degree, and the variance among the outcrossed families was significant only on the more productive site. The performance of self-families for diameter was highly stable between sites. This suggests that, for species with mixed mating systems, environmentally stable inbreeding effects in open-pollinated progenies may tend to mask the additive genotype-by-environment interaction for fitness traits and the adaptive response to the environment.

A Robust Statistical Method to Detect Null Alleles in Microsatellite and SNP Datasets in Both Panmictic and Inbred Populations

Null alleles are common technical artifacts in genetic-based analysis. Powerful methods enabling their detection in either panmictic or inbred populations have been proposed. However, none of these methods appears unbiased in both types of mating systems, necessitating a priori knowledge of the inbreeding level of the population under study. To counter this problem, I propose to use the software FDist2 to detect the atypical fixation indices that characterize markers with null alleles. The rational behind this approach and the parameter settings are explained. The power of the method for various sample sizes, degrees of inbreeding and null allele frequencies is evaluated using simulated microsatellite and SNP datasets and then compared to two other null allele detection methods. The results clearly show the robustness of the method proposed here as well as its greater accuracy in both panmictic and inbred populations for both types of marker. By allowing a proper detection of null alleles for a wide range of mating systems and markers, this new method is particularly appealing for numerous genetic studies using co-dominant loci.

Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean FIS values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.

Genetic diseases in the Tunisian population

Tunisia is one of the North African countries, geographically situated in a central position at the crossroad between Africa and Europe. The demographic features of the Tunisian population include among others high rates of consanguinity. We report, here on the spectrum of genetic diseases in Tunisia. The review of the literature, including other available information (gray literature) showed that there are at least 346 genetic disorders for which cases have been identified in the Tunisian population. Among these, 62.9% are autosomal recessive, 23% autosomal dominant, 5.4% X-linked, and the remaining are of Y-linked, mitochondrial, and unknown mode of transmission. Fifty percent of the reported conditions in this study are caused by at least one mutation. For autosomal recessive diseases, most of the mutations were identified at homozygous state among the affected individuals. Part of the mutations was the result of a founder effect; these are the consequences of the high rate of consanguinity. The congenital malformations, diseases of the nervous system and metabolic disorders are the major groups of genetic diseases affecting the Tunisian population. The large spectrum of diseases and their relatively high frequency could be explained by the high degree of inbreeding and the presence of multiple mutations, either allelic or in different genes. This is due to the richness of the genetic background of the studied population. A multidisciplinary approach is essential to develop adequate preventive programmes adapted to the social, cultural, and economic context.

Colony Breeding System Influences Cuticular Bacterial Load of Formosan Subterranean Termite (Isoptera: Rhinotermitidae) Workers

The goal of this study was to test whether the breeding system and/or the degree of inbreeding of field colonies of the Formosan subterranean termite, Coptotermes formosanus, Shiraki (Isoptera: Rhinotermitidae) influences bacterial load on the cuticle of foraging workers. We enumerated bacterial load on the cuticle of groups of workers foraging in 20 inground monitoring stations surrounding the French Market in New Orleans, LA, and identified bacteria species using 16S rRNA gene sequencing. We used microsatellite genotyping to assign the 20 worker groups to seven simple family colonies (headed by a single pair of reproductives) and four extended family colonies (headed by multiple inbreeding reproductives) with a wide range of degrees of inbreeding. Workers from extended family colonies had a higher bacterial load than those from simple family colonies; however, bacterial load was not significantly correlated to the degree of inbreeding, possibly because of confounding factors in colony life history, such as age and/or size of colonies. Colonies with high bacterial load did not have a higher proportion of entomopathogens, and thus, bacterial load is not necessarily an indicator for disease risk. The majority of bacteria cultured from the cuticle of termites were soil bacteria with no known pathology against termites.

Genetic variation and clonal diversity of the endangered aquatic fern Ceratopteris pteridoides as revealed by AFLP analysis

Ceratopteris pteridoides (Hook.) Hieron. is an endangered aquatic homosporous fern in China. Genetic diversity and structure of eight populations collected from the mid-lower reaches of Yangtze River were investigated using amplified fragment length polymorphisms (AFLPs). A low level of gene diversity was found at the population level (Pp=17.4%, HE=0.039 and I=0.063), which possibly resulted from its high degree of inbreeding, clonal growth and short life history of this species. C. pteridoides contained high clonal diversity (PD=0.757, D=0.992). High population differentiation was revealed by partitioning of genetic diversity (GST=0.707), and the AMOVA analysis consistently showed that 72.3% of the total genetic diversity was attributable to among-population diversity. Based on the genetic information from UPGMA cluster and principal coordinate analysis, two management units have been identified, and translocation within each management unit is recommended.

Immotile Short‐Tail Sperm Defect in Nelore (Bos taurus indicus) Breed Bulls

This case study reported the presence of short tail sperm defect in the semen of three Nelore breed bulls. The sperm presented 0% of motility in the three animals evaluated and a total of 70%, 61% and 34% of pathologies of the intermediate piece of the tail respectively for animals 1, 2 and 3. It was identified that animals 2 and 3 had high degree of inbreeding, although no relationship was found with animal 1. Animal 2 was the only one that presented inbreeding coefficient (6.25%). His half-sib (animal 3) and animal 1, from the same herd, had shown no inbreeding, showing that inheritance is not the only determinant factor for its incidence on Nelore males.

Development of Microsatellites for Genetic Analyses and Population Assignment of the Cat Flea (Siphonaptera: Pulicidae)

Cat fleas, Ctenocephalidesfelis (Bouché) (Siphonaptera: Pulicidae), are common ectoparasites of companion animals that negatively impact their hosts directly by causing dermatitis and blood loss during feeding and indirectly through the potential transmission of disease causing agents. We isolated and characterized seven novel microsatellite loci from a partial genomic library of the cat flea enriched for di-, tri-, and tetranucleotide repeats. We screened these loci in cat fleas from two laboratory colonies and one wild-caught population collected at a temporary animal shelter (Parker coliseum) in Baton Rouge, LA. Six loci were polymorphic, with two to 15 alleles per locus and an average observed heterozygosity of 0.21 across populations. Although the two laboratory cat flea colonies were isolated from each other for many years, they did not significantly differ in their genotypic composition. The cat flea population from Parker coliseum was genetically different from the laboratory colonies, but also showed high degrees of inbreeding. Multilocus genotypes of the polymorphic loci were sufficient to assign over 85% of cat fleas to their population of origin. Genetic markers for flea population identity will allow further studies to examine the origins and movement of cat fleas with important genetic traits such as insecticide resistance or pathogen susceptibility. The use of microsatellites also could determine if there are host-specific strains of cat fleas and add insight into the development of the different subspecies of C. felis.

Analysis of yield and oil from a series of canola breeding trials. Part I. Fitting factor analytic mixed models with pedigree informationThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

In this paper multiplicative mixed models have been used for the analysis of multi-environment trial (MET) data for canola oil and grain yield. Information on pedigrees has been included to allow for the modelling of additive and nonadditive genetic effects. The MET data set included a total of 19 trials (synonymous with sites or environments), which were sown across southern Australia in 2007 and 2008. Each trial was designed as a p-rep design using DiGGeR with the default prespecified spatial model. Lines in their first year of testing were unreplicated, whereas there were two or three replications of advanced lines or varieties. Pedigree information on a total of 578 entries was available, and there were 69 entries that had unknown pedigrees. The degree of inbreeding varied from 0 (55 entries) to nearly fully inbred (337 entries). Subsamples of 2 g harvested grain were taken from each plot for determination of seed oil percentage by near infrared reflectance spectroscopy. The MET analysis for both yield and oil modelled genetic effects in different trials using factor analytic models and the residual plot effects for each trial were modelled using spatial techniques. Models in which pedigree information was included provided significantly better fits to both yield and oil data.

Analysis of 11 tetrameric STRs in wild boars for forensic purposes

STR profiling of animal species has a wide range of applications, including forensic identification, wildlife preservation, veterinary public health protection and food safety. We tested the efficacy of a multiplex PCR-based assay including 11 porcine-specific tetrameric STRs in a population sample of wild boars ( n = 142) originating from Piedmont (North West Italy). Multiple deviations from Hardy–Weinberg expectations were observed, mostly due to a reduction in observed heterozygosity indicative of a high degree of inbreeding. A value of θ of 0.046 and an inbreeding coefficient of 0.089 were estimated. Combined power of discrimination and probability of exclusion values for the STR panel were 0.9999999999996 and 0.99989. In order to test the suitability of the method for meat traceability purposes, a domestic pig reference sample ( n = 412), consisting of commercial lines commonly used in the meat production process, was also typed. A Bayesian cluster analysis carried out using the observed genotypes, showed a percentage of correct subspecies assignment of individual samples of 0.974 for wild boars and 0.991 for pigs, thus demonstrating the usefulness of the multiplex STR-typing system for discrimination purposes.

Coexistence of mal de Meleda and congenital cataract in a consanguineous Tunisian family: two case reports

IntroductionMal de Meleda is a rare form of palmoplantar keratoderma, with autosomal recessive transmission. It is characterized by diffuse erythema and hyperkeratosis of the palms and soles. Recently, mutations in the ARS (component B) gene (ARS, MIM: 606119) on chromosome 8q24.3 have been identified in families with this disorder. Congenital cataract is a visual disease that may interfere with sharp imaging of the retina. Mutations in the heat-shock transcription factor 4 gene (HSF4; MIM: 602438) may result in both autosomal dominant and autosomal recessive congenital cataracts.Case presentationA Tunisian family with two female siblings aged 45 and 30 years, presented with a clinical association of mal de Meleda and congenital cataract. The two patients exhibited diffuse palmoplantar keratodermas. One of them presented with a total posterior subcapsular cataract and had a best corrected visual acuity at 1/20 in the left eye and with the right eye was only able to count fingers at a distance of one foot. The other woman had a slight posterior subcapsular lenticular opacity and her best corrected visual acuity was 8/10 in the right eye and with her left eye she was only able to count fingers at a distance of one foot. A mutational analysis of their ARS gene revealed the presence of the homozygous missense mutation C99Y and two single nucleotide polymorphisms (-55G>C and -60G>C). The splice mutation (c.1327+4A-G) within intron 12 of the HSF4 gene, which has been previously described in Tunisian families with congenital cataract, was not found in the two probands within this family.ConclusionTo the best of our knowledge, such original clinical association has not been reported previously. The association of these two autosomal recessive diseases might have occurred in this family due to a high degree of inbreeding. The C99Y mutation may be specific to the Tunisian population as it has been exclusively reported so far in only three Tunisian families with mal de Meleda.

Sensitivity of Lake Sturgeon Population Dynamics and Genetics to Demographic Parameters

AbstractUncertainty in population parameters can make managing fisheries difficult, especially for long‐lived species such as lake sturgeon Acipenser fulvescens. Models can be used to explore population parameter uncertainty and how uncertainty affects demographic and genetic population outputs through the use of sensitivity analyses. The objective of this study was to determine which lake sturgeon population parameters have the greatest influence on demographic characteristics, including rates of extinction and percentage of populations increasing from their initial size, and population genetic characteristics, including percentage of unique alleles retained and average inbreeding coefficient. An individual‐based modeling approach that represented demographic and genetic processes was used to achieve this objective. Individual lake sturgeon were tracked throughout the modeling process with unique identifiers, allowing for the determination of the degree of inbreeding and the number of unique alleles retained. Sensitivity analyses were performed by changing one parameter at a time across a range of plausible values while holding all of the other parameters at their nominal values. All responses were hypersensitive to young‐of‐the‐year mortality, post–young‐of‐the‐year mortality, age at first maturation for females, and probability of mating for females. The post–young‐of‐the‐year mortality rate was the most sensitive of all of the population parameters. The outputs were relatively insensitive to changes in the age at first maturation for males and the probability of mating for males. Sensitivity was dependent upon the initial population size, with population parameters having differing sensitivities with respect to other parameters for smaller and larger population sizes. The demographic and genetic outputs were related to one another via similar relationships for each of the population sizes. These analyses should be used to target rehabilitation efforts on altering population parameters with the largest influence on population persistence and genetic integrity.

Gene Conversion and DNA Sequence Polymorphism in the Sex-Determination Gene fog-2 and Its Paralog ftr-1 in Caenorhabditis elegans

Gene conversion, a form of concerted evolution, bears enormous potential to shape the trajectory of sequence and functional divergence of gene paralogs subsequent to duplication events. fog-2, a sex-determination gene unique to Caenorhabditis elegans and implicated in the origin of hermaphroditism in this species, resulted from the duplication of ftr-1, an upstream gene of unknown function. Synonymous sequence divergence in regions of fog-2 and ftr-1 (excluding recent gene conversion tracts) suggests that the duplication occurred 46 million generations ago. Gene conversion between fog-2 and ftr-1 was previously discovered in experimental fog-2 knockout lines of C. elegans, whereby hermaphroditism was restored in mutant obligately outcrossing male-female populations. We analyzed DNA-sequence variation in fog-2 and ftr-1 within 40 isolates of C. elegans from diverse geographic locations in order to evaluate the contribution of gene conversion to genetic variation in the two gene paralogs. The analysis shows that gene conversion contributes significantly to DNA-sequence diversity in fog-2 and ftr-1 (22% and 34%, respectively) and may have the potential to alter sexual phenotypes in natural populations. A radical amino acid change in a conserved region of the F-box domain of fog-2 was found in natural isolates of C. elegans with significantly lower fecundity. We hypothesize that the lowered fecundity is due to reduced masculinization and less sperm production and that amino acid replacement substitutions and gene conversion in fog-2 may contribute significantly to variation in the degree of inbreeding and outcrossing in natural populations.

The challenge of improving patient safety in primary care

A retrospective study was conducted on prenatal and postnatal mortality among the populations of seven cities in the Pakistani province of Punjab. Consanguineous marriages were strongly favoured and the coefficients of inbreeding (F) for the present generation in each locality ranged from 0.0236 to 0.0286. There was a highly significant relationship between the degree of inbreeding and mortality, with most consanguinity related deaths reported in the neonatal, infantile, and childhood periods. The findings strongly suggest that consanguinity may play a major role in the high rates of postnatal mortality observed in Pakistani communities now resident in the United Kingdom.

Population genetic analysis of White Park Cattle in Germany

Abstract. The population of White Park Cattle in Germany is composed of 11 males and 33 females. This group of cattle has been analysed with regards to generation intervals, coancestry, and inbreeding on the basis of three generations of ancestors. The average interval between the current and the parental generation amounts to seven years. The average coefficient of coancestry in the population is estimated to be 18 % and the average degree of inbreeding at 16 %. The rate of inbreeding in the last generation is approximately 12 %. These values exceed those reported for most breeds of production animals.

Communal spawning leads to high potential for inbreeding in gadoid aquaculture

The potential for relatedness to play a role in haddock ( Melanogrammus aeglefinus) mate selection was tested in order to examine the potential for inbreeding in the culturing of this species. A total of 14 egg batches were produced in a communal spawning tank containing three full-sibling families over a 22 day period. Three females and seven males participated in these matings among the five females and eight males present. Based on genotyping results of fertilized eggs, there was no preference for mating with unrelated individuals (i.e. no avoidance of mating with siblings). The maximum number of males contributing to the fertilization success of an egg batch was three but with a single dominant male fertilizing a majority of the eggs for each batch. Only three of the egg batches produced appeared to have been fertilized entirely by a single male. The degree of relatedness among F 1 commercial haddock broodstock was investigated relative to that of wild Bay of Fundy haddock. This comparison was intended to estimate how rapidly inbreeding could accumulate in a haddock population under cultivation when limited control was exerted over the actual communal mating. Allele richness (standardized numbers of alleles) was markedly lower in the aquaculture samples relative to the wild population (by approximately 25%). The size-selected F 1 haddock sample exhibited slightly lower levels of observed heterozygosity and gene diversity than a random sample of F 1 haddock, but marginally higher allele richness. The reduced family diversity coupled with the fact that haddock do not appear to avoid mating with kin could potentially lead to a high degree of inbreeding in the absence of the infusion of additional wild broodstock.

Genetic studies of IDDM in BB rats: the incidence of diabetes in F2 and first backcross hybrids allows rejection of the recessive hypothesis.

The BB rat spontaneously develops an IDDM with many analogies to human IDDM, i.e. the genetic basis is a puzzle, since more than one mode of inheritance of IDDM in BB rats has been proposed. These different proposals reflect the heterogeneity of BB rats used for genetic studies. This prompted us to investigate the inheritance of IDDM in two subpopulations of BB rats (BB/OK and BB/PhiK) by crossing studies with the production of (diabetic BB x LEW 1.A) F1, F2 generations and of first backcross hybrids onto BB (B1BB) and LEW.1A (B1A) rats respectively. Both BB rat subpopulations were different in origin, degree of inbreeding, incidence and age at onset of diabetes and in certain immunologic, metabolic and hematologic traits. All hybrids were serotyped and checked for diabetes by determination of urine and plasma glucose twice weekly up to an age of 200 days. None of the F1 and B1A hybrids developed diabetes. Some cases were observed in the F2 hybrids with a different incidence in the two subpopulations (2.3% in BB/OK, 11.0% in BB/PhiK). The percentage of diabetes in the B1BB hybrids was 13.8% (BB/OK) and 24.0% (BB/PhiK) respectively. All diabetic hybrids were characterized by at least one RT1uv haplotype which was derived from the original BB animals. These results demonstrated clearly (1) that the mode of inheritance depends on the genotype of the animals observed and (2) simple autosomal-recessive genetics cannot be accepted for BB rat diabetes.(ABSTRACT TRUNCATED AT 250 WORDS)